Séminaire interne

22 juin 2018, 10:00 AM (Room BAT5 02/022)

Marc Chakiachvili, "Why and how to choose your IDE (integrated development environment)"

Résumé

"An integrated development environment (IDE) is a software application that provides comprehensive facilities to computer
programmers for software development. An IDE normally consists of
a source code editor, build automation tools and a debugger. Most
modern IDEs have intelligent code completion. Some IDEs contain a
compiler, interpreter, or both. Sometimes a version control system
are integrated. Many modern IDEs also have a class browser, an
object browser, and a class hierarchy diagram, for use in object-oriented software development."

Well, that's only Wikipedia IDE definition....
Clearly when developing complex pieces of software, use of an IDE
can definitely simplify your programmer's life and reduce the time
you spend developing...
- So how and what should you consider before choosing the right
IDE for your programs ?
- Simple extensible Text Editor, or choose big and string IDE to
ease your development ?
- I'll show you the best ever IDE, everyone should use ! in my opinion, which is obviously unbiased !

14 juin 2018, 13:30 AM (Room BAT5 02/022)

Eric Rivals, "Hierarchical Overlap Graph"

Résumé

Given a set of finite words, the Overlap Graph (OG) is a complete
weighted digraph where each word is a node and where the weight of an
arc equals the length of the longest overlap of one word onto the
other (Overlap is an asymmetric notion). The OG serves to assemble DNA
fragments or to compute shortest superstrings which are a compressed
representation of the input. The OG requires a space is quadratic in
the number of words, which limits its scalability. The Hierarchical
Overlap Graph (HOG) is an alternative graph that also encodes all
maximal overlaps, but uses a space that is linear in the sum of the
lengths of the input words. We propose the first algorithm to buildthe HOG in linear space for words of equal length.

25 janvier 2018, 10:00 AM (Room BAT5 01/156)

14 décembre 2017, 10:00 AM (Room BAT5 0/156)

Résumé

Comparaison de pipelines d'analyse de variants génomiques

30 november 2017, 10:00 AM (Room BAT5 02/156)

Marie-Cécile Robert, "Presentation of the CRISPR/CAs9 system"

Résumé

Marie-Cécile works in the MGC (Montpellier Genomic Collection) plateform of the IGMM. She will introduce us to the famous CRISPR/CAs9 system, its applications and why it is a revolution in molecular biology.

Résumé

22 june 2017, 10:00 AM (Room BAT5 2/022)

Marc Chakiachvili, "Why and how to choose your IDE (integrated development environment)"

Résumé

An integrated development environment (IDE) is a software application that provides comprehensive facilities to computer programmers for software development. An IDE normally consists of a source code
editor, build automation tools and a debugger. Most modern IDEs have intelligent code completion. Some IDEs contain a compiler, interpreter, or both. Sometimes a version control system are integrated.Many modern IDEs also have a class browser, an object browser, and a class hierarchy diagram, for use in object-oriented software development."

Well, that's only Wikipedia IDE definition....

Clearly when developing complex pieces of software, use of an IDE can definitely simplify your programmer's life and reduce the time you spend developing...

- So how and what should you consider before choosing the right IDE for your programs ?
- Simple extensible Text Editor, or choose big and string IDE to ease your development ?- I'll show you the best ever IDE, everyone should use ! in my opinion, which is obviously unbiased !

20 april 2017, 10:00 AM (Room: BAT5 01/124)

Résumé

Do you have a program that operates on data produced by another program?
Snakemake is an efficient way to deal with interactions between a group of programs that depend on each other.
Some benefits of Snakemake are:
1. python-based syntax (little syntax specific to snakemake)
2. automatic parallelization of calls 3. easily rerun only the necessary parts of an experiment after changes to code or input

I will present the basics of Snakemake and go through a simple example.

16 march 2017, 10:00 AM (Room: BAT5 02/022)

Rodrigo-antonio Canovas-barroso, "Debate about Compressed Structures"

Résumé

A compressed structure is a data structure modified to take up little space, besides providing direct access
and functionalities to answer certain queries on the stored data without need to decompress them.
Nowadays it has become of vitally important to operate on compressed data.
This is mainly because the information handled has grown exponentially and,
as an aggravating circumstance, secondary storage technology has not evolved enough in terms of speed.
Currently, main memory access is estimated at 10 ns, whereas disk access is estimated at 10^7 ns.
The speed difference is so vast that it is preferable to pay a moderate cost of access to a slower compressed structure,that it fits in main memory, than to make constant access to disk.

In this context compressed structures make more sense, because by using a smaller space,
more information can be handled in main memory by paying a lower operating cost than
managing the same information efficiently on disk. However, still remains the questionfor how long these structures will be still needed.

8 december 2016, 10:00 AM (Room: BAT5 02/022)

Laurent bréhélin, "Cell biology by the numbers"

Résumé

"One of the central missions of our book is to serve as an entry point
that invites the reader to explore some of the key numbers of cell
biology. We imagine readers of all kinds with different approaches:
seasoned researchers who simply want to find the best values for some
number of interest or beginning biology students who wish to supplement
their introductory course materials. In the pages that follow, we
provide several dozen vignettes, each of which focuses on quantities
that help us think about sizes, concentrations, energies, rates,
information content and other key quantities that describe the livingworld." http://book.bionumbers.org/

24 november 2016, 10:00 AM (Room: BAT5 01/124)

Fabio Pardi, "SIMONS human diversity project"

Résumé

The SIMONS project completed the 1000 human project by sequencing many
ancestral Asian and Oceania populations. Their results highlights the complexity
of ancestral Homo sapiens cross-breeding which occured at different times
and different continents (sapiens, neanderthalis and denisova).A nice example of coalescence models application will be discussed.

20 october 2016, 10:00 AM (Room: BAT5 02/022)

Benjamin Linard, "Science and social networking"

Résumé

Social networks are more and more used by scientists to spread
their research (Twitter, LinkedIn, Facebook). But social networks specifically
targeted to scientists are now appearing (Google scholar, Researchgate).
Are these useful and can be considered as a research tool ?
Or are they just a consequence of the "mediatic science" in which we livemore and more, forgetting sometimes the purposes of science ?